Natural resource management research has to evolve from a focus on plans, maps, and regulations to an acknowledgment of the complex, sometimes chaotic, reality in the field, with a large number of actors making their own decisions. As outside actors, we can only try to facilitate and support a process of negotiation among the stakeholders. Such negotiation involves understanding the perspectives of all stakeholders, analyzing complementarities in views, identifying where differences may be settled by “science,” where science and social action can bring innovative alternatives for reconciliation, and where compromises will be necessary to move ahead. We distinguish between natural resource management problems at village level, within country, or transboundary, and those that relate local stakeholder decisions to global issues such as biodiversity conservation. Tree-based systems at plot or landscape level can minimize conflicts between private and public interests in local environmental services, but spatial segregation of functions is an imperative for the core of global biodiversity values. The complex agroforests developed by farmers as alternatives to food-crop-based agriculture integrate local and global environmental functions, but intensification and specialization may diminish these non-local values. For local biodiversity functions, a medium-intensity “integrate” option such as agroforests may be superior in terms of resilience and risk management.